Scientists discover RNA phenomenon that challenges dogma

Some RNA molecules spend
time in a restful state akin to hibernation rather than automatically carrying
out their established job of delivering protein-building instructions in cells,
new research suggests.

And instead of being a
fluke or a mistake, the research suggests that this restful period appears to
be a programmed step for RNA produced by certain types of genes, including some
that control cell division and decide where proteins will work in a cell to
sustain the cell's life.

This could mean that
protein production in cells is not as clear-cut as biology textbooks suggest,
scientists say.

"This could mean there are
more variations to the proteins in our bodies than we realize; it means that
RNAs can be stored and reactivated and we don't know what biological process
that affects—it could influence embryonic development, or neurological activity,
or even cancer," says Daniel Schoenberg, professor of molecular and cellular
biochemistry at Ohio State University and lead author of the study.

Schoenberg and colleagues
discovered this phenomenon by tracing the origins of a cap-like structure on messenger
RNA (mRNA) that is known to coordinate most of this RNA molecule's short life. Messenger
RNA is manufactured in a cell's nucleus and each mRNA contains the instructions
needed to produce a specific protein that a cell needs to live.

Until now, scientists have
believed that once an mRNA is no longer needed to make protein, the cap comes
off and the molecule is degraded, its job complete. But Schoenberg's laboratory
discovered in 2009 that some mRNAs that were thought to be degraded were
instead still present in the cell, but they were missing part of their sequence
and had caps placed back on the newly formed ends. Because these mRNAs were in
the cytoplasm, the changes had to happen there rather than inside the nucleus.

In this new study, the
researchers were looking for further evidence of these apparent rogue mRNAs,
but instead they found that a completely unexpected biological process occurs
before some proteins are even a glimmer in a gene's eye: The uncapping and recapping
of mRNAs outside the nucleus results from a cap recycling operation in the cell
cytoplasm. This process appeared to enable certain RNAs to pause, without being
degraded, before launching protein production.

"What this discovery tells
us is a complete fundamental reworking of the relationship between a gene,
messenger RNA and a protein. It's more complicated than we realize," Schoenberg
says.

The research is published
online in Cell Reports.

That fragments of mRNA
could exist at all in the cell's main body was first reported by other
scientists in 1992. Years later, Schoenberg asked a postdoctoral researcher in
his laboratory to revisit these unexpected RNA fragments and confirm they exist. The
postdoctoral researcher's experiments showed that these mRNA, thought to be the
dregs left over from their degradation, had caps on them—suggesting they still
had the potential to function in protein production. Schoenberg, also director
of Ohio State's Center for RNA Biology, has been investigating this cytoplasmic
capping operation ever since.

In 2009, he and colleagues
reported the discovery of two enzymes in the cell's main body that would enable
mRNA capping to occur completely outside the nucleus and in the cytoplasm
instead.

In the current studies,
Schoenberg sought to determine the physiological significance of this capping
operation. The researchers engineered a way to block cytoplasmic capping in
cells in the laboratory and then looked at changes in more than 55,000 RNAs.

This interference with
cytoplasmic capping revealed that two different types of pathways could exist
in the cells—some mRNAs remained stable without their caps, while others
without caps were rapidly destroyed. This finding indicated that mRNAs can lose
their caps in the cytoplasm and at some point get recapped. With further
experimentation, the researchers determined that only some mRNAs lost their
caps in the cell body.

"It's not all of any
particular message that’s uncapped, just a portion of a message," Schoenberg
says. "We wanted to show that we have uncapped RNAs in the cell and they are
not degraded. It means they’re stored that way."

This finding offered hints
that there is a higher order to this phenomenon, and that some mRNAs
purposefully rest in an uncapped state without being degraded by enzymes within
the cell whose job is to remove them. It also suggested that as the capping
circumstances change inside the cell body, signals from genes might undergo
change that allows for two or more proteins, one being shorter than the other,
to be made from the same mRNA.

"We have always thought
that one gene would give an mRNA for one kind of protein. But what we have
found makes us wonder if multiple proteins could be made from each of the
messenger RNAs that undergo decapping and recapping in the cytoplasm,"
Schoenberg says.

The researchers used
bioinformatics technology to determine which genes were manufacturing mRNAs
that could exist in this uncapped and recapped state in the cytoplasm. These
genes included those that control some of the most basic elements of cell
survival: They determine the location of proteins and RNAs within the cell and,
perhaps most significantly, the mitotic cell cycle—part of the process of cell
division.

"It wasn't random. It was
very specific," Schoenberg says. "There are specific families of mRNAs that are
regulated in this way, and that has ramifications for how proteins are
expressed and regulated."

As an example, he cited how
neurons communicate messages across vast distances to other nerve cells. It is
known that mRNAs are deliberately kept in a silent state while they travel
from, for example, the spinal cord to the fingertip, where they are then
activated to make new proteins.

"What would the condition
be of the mRNA to keep it silent? The possibility is it doesn’t have a cap on
it, and if it doesn't, it can’t be translated. Maybe cytoplasmic capping in
neurons is a function that allows that message to be translated at just the
right time," Schoenberg says.

Or, in the case of cancer: "What if one of the things that happens is you are making shortened proteins
instead of full-length proteins and the regulatory part of the protein is
missing in the shortened protein? If that's true, can you interfere with this
process and interfere with malignancy as a result?"

For now, these scientists
can only speculate about what this unexpected biological process really means.
Schoenberg's laboratory plans to investigate the phenomenon more thoroughly in
a line of breast cancer cells.